BioSecondaryStructure.h

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/****************************************************************************
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The BioBhasha : The Biologist's Programming Language 
Version 1.0 (19th December 2001)
Prasad, B.V.L.S.
Contact: burrashiva@yahoo.com
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*****************************************************************************/

#ifndef BIOSECONDARYSTRUCTURE_H
#define BIOSECONDARYSTRUCTURE_H

#include "BioPdbHelix.h"
#include "BioPdbSheet.h"
#include "BioPdbTurn.h"
#include <vector>
#include <string>

class BioSecondaryStructure
{
        vector<BioPdbHelix>helix_;
        vector<BioPdbSheet>sheet_;
        vector<BioPdbTurn>turn_;
        string FILE;
        
     
     void countChainIds(void);
     string chainIds;   
     void setSecStr(vector < string > );  

        public: 
                BioSecondaryStructure(const string& );
        

      int getNumberOfSheets();
                int getNumberOfHelices();
                int getNumberOfTurns();

                int getNumberOfHelices(char chai_id);
                int getNumberOfTurns(char chai_id);

                int getNumberOfHelices(int index);
                int getNumberOfTurns(int index);


                char getSecondaryStructureChainId(int index);
      int getNumberOfSecondaryStructureChainIds();

                void getSheetDirectionCosines(int);

                void showHelixDirectionCosines(int);
                void showHelixDirectionCosines(BioProteinChain&,int);

                vector<BioMatrix> getHelixDirectionCosines();

                void showSheetIds(ostream& = cout);
                void showHelixIds(ostream& = cout);
                void showTurnIds(ostream& = cout);

                int getHelixIdIndex(const string& );
                int getTurnIdIndex(const string& );
                int getSheetIdIndex(const string& );

                BioPdbHelix getHelix(char ch_id ,int helix_index);
                BioPdbTurn getTurn(char ch_id ,int);
                BioPdbSheet getSheet(int);

                BioPdbHelix getHelix(int ch_id_index,int helix_index);
                BioPdbTurn getTurn(int ch_id_index,int turn_index);



                void showAllHelixSequences(ostream& = cout);
                string getHelixSequence(int index);

                void showAllTurnSequences(ostream& = cout);
                string getTurnSequence(int index);

                void showAllSheetSequences(ostream& = cout);
                string getSheetSequence(int shIndex, int strIndex);

                void showSecondaryStructure(int index, BioPostScript& ps,float startx=50,float starty=800,float width=475);
                void showSecondaryStructure(char index, BioPostScript& ps,float startx=50,float starty=800,float width=475);

    string getSecondaryStructureSequence(int index);
    string getSecondaryStructureSequence(char chainID);



//              BioPdbSheet getStrand(int chainid, int);
//              BioPdbSheet getStrand(char chainid, int);
 //     int getNumberOfStrands(int chain_index);
//      int getNumberOfStrands(char chai_id);
};

#endif